Aboveground farming is fun. Part of the reason it's fun is because you can have so many crops to choose from, compared to underground farming where you get the same 6 crops in every game in every eco-system. It would be cooler if you could discover new underground crops as you start exploring the caverns.
One of the things that annoys me about underground farming compared to aboveground farming is that due to the seasonal nature of pigtails, it's difficult to get a constant, trade-able textile industry set up. But if you have access to aboveground crops like cotton, jute, ramie or hemp (woo), a meager farmland will have you swimming in cloth. This is doubling annoying because an underground crop really should not be affected by seasons, while an aboveground crop really should.
So ideas for rare underground crops include:
Textile crops that grow year-round
Textile crops that grow during the seasons that pigtails don't grow
More die colors
High quality crops that grow during only one season. (note that this would also make them hard to find, since you'd have to gather plants during the right season)
Poison plants (if extracting poison ever becomes useful)
Plants that can only be turned into booze, but make the best booze
Plants that have to be cooked to be edible, but taste delicious
Plants that produce odd substances, like wood, wax, gems, tallow, leather, cheese, resin or rubber.